cell_type_name = "CD8T"
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 24.0 25.0 26.0 25.8 27.0 28.0
## [1] 40
## [1] 24 24 24 24 25 25 25 25 25 25 25 25 25 25 25 25 25 26 26 26 26 26 26 26 26
## [26] 26 26 26 27 27 27 27 27 27 27 27 27 27 27 28
## [1] 1032
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "C7orf55"
## [1] "FMC1-LUC7L2" "FMC1"
## [1] "MARS"
## [1] "MARS1" "SLA2"
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "APITD1"
## [1] "CENPS-CORT" "CENPS"
## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"
##
## FALSE TRUE
## 1120 139
##
## FALSE TRUE <NA>
## 71 1049 139
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: ZNRD1 POLR1H
## 2: C2orf43 LDAH
## 3: FAM45A DENND10
## 4: MTERF MTERF1
## 5: NARG2 ICE2
## 6: C6orf203 MTRES1
## 7: HRSP12 RIDA
## 8: FOPNL CEP20
## 9: WARS WARS1
## 10: LINS LINS1
## 11: RRNAD1 METTL25B
## 12: FAM122B PABIR2
## 13: WDYHV1 NTAQ1
## 14: HIST1H2BD H2BC5
## 15: AGPAT6 GPAT4
## 16: C1orf123 CZIB
## 17: KIAA1841 SANBR
## 18: C2orf44 WDCP
## 19: TMEM155 SMIM43
## 20: C7orf55 FMC1-LUC7L2
## 21: C9orf89 CARD19
## 22: C11orf82 DDIAS
## 23: XRCC6BP1 ATP23
## 24: MARS MARS1
## 25: C19orf55 PROSER3
## 26: HIST1H2AE H2AC8
## 27: QARS EPRS1
## 28: APITD1 CENPS-CORT
## 29: CCDC101 SGF29
## 30: PDDC1 GATD1
## 31: EFCAB4A CRACR2B
## 32: EIF2S3L EIF2S3B
## 33: HIST1H2BC H2BC5
## 34: WRB GET1
## 35: TMEM194B NEMP2
## 36: HIST1H4C H4C3
## 37: HIST1H4J H4C11
## 38: ZNF720 KRBOX5
## 39: HIST1H2BH H2BC9
## 40: FAM49A CYRIA
## 41: TTC37 SKIC3
## 42: C1orf85 GLMP
## 43: C9orf114 SPOUT1
## 44: HIST2H2AA4 H2AC19
## 45: HIST2H2BF H2BC18
## 46: C10orf128 TMEM273
## 47: TCTEX1D2 DYNLT2B
## 48: C17orf89 NDUFAF8
## 49: PHBP3 PHB1P3
## 50: SEPT7P7 SEPTIN7P7
## 51: LINC00493 SMIM26
## 52: HIST1H2BN H2BC15
## 53: ATP5J2 ATP5MF
## 54: AKAP2 PALM2AKAP2
## 55: WDR65 CFAP57
## 56: SRP14-AS1 SRP14-DT
## 57: CTC-436P18.1 SMIM15-AS1
## 58: HIST1H3G H3C8
## 59: EFTUD1P1 EFL1P1
## 60: ATP5A1P3 ATP5F1AP3
## 61: CCDC109B MCUB
## 62: C1orf63 RSRP1
## 63: TMEM66 SARAF
## 64: PCNXL2 PCNX2
## 65: ACRC GCNA
## 66: AMICA1 JAML
## 67: PRMT10 PRMT9
## 68: FAM102A EEIG1
## 69: SELM SELENOM
## 70: NBPF16 NBPF15
## 71: RPL9P9 RPL9P8
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]
dim(gene_info)## [1] 1259 3
## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1
## 3: ICA1 ICA1 ICA1
## 4: NDUFAF7 NDUFAF7 NDUFAF7
## 5: ST7 ST7 ST7
## t1
## 1 2
## 1255 2
## sym_in_data sym_limma gene_symbol
## 1: HIST1H2BD H2BC5 H2BC5
## 2: HIST1H2BC H2BC5 H2BC5
## 3: RPL9P8 RPL9P8 RPL9P8
## 4: RPL9P9 RPL9P8 RPL9P8
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]] = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp" "immune"
## reactome go_bp immune
## 1692 7647 5219
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
##
## $immune
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5 162 193 197 199 199 200 200 200 200 1992
## [1] 1259 3
## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=120)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "MAP4K5" "PAFAH1B3" "SPTLC2" "CAPN15" "PIEZO1" "RASSF4"
## [7] "CACYBP" "CCR2" "NUP85" "UROD" "NPHP4" "HRSP12"
## [13] "ANXA1" "ASNSD1" "MZT2B" "CENPH" "RNF207" "C1orf123"
## [19] "RNF25" "LRRC28" "UBB" "HSPA1B" "MYCBP" "TMEM63A"
## [1] 2
## [1] "IL4R" "UTP6" "ACVR1" "SMUG1" "GLUL"
## [6] "GNG4" "ZNF816" "RPS27AP2" "CTB-33G10.1" "TXK"
## [11] "ARRDC2" "RASGRF2" "EGR1" "ACVR2A" "FOSB"
## [16] "JUND" "SKIL" "SORL1" "SGSM2" "GNAQ"
## [21] "LDLRAP1" "DHRS3" "TC2N" "TMEM150A" "DNHD1"
## [1] 3
## [1] "CCL3" "TIMM21" "WDR7" "THOC5" "PON2" "KLRB1"
## [7] "BRD8" "EMG1" "CCL4" "ACTR10" "KLRC1" "GCHFR"
## [13] "CXCL13" "PANK4" "C19orf47" "EXTL2" "GTSF1" "METTL18"
## [19] "WRB" "COA3" "CMC1" "CCL4L2" "MSH5" "CCL4L1"
## [25] "CCL3L1" "KLRC2"
## [1] 4
## [1] "ID3" "PARP2" "MMS22L" "PLIN2"
## [5] "ATF3" "HIST1H2BC" "PLA2G6" "HIST2H2AA4"
## [9] "HIST1H2BN" "HIST1H3G" "RP11-386G11.10" "IFRD1"
## [13] "RGCC" "NR4A3" "RASGEF1B" "NR4A2"
## [17] "TIPARP" "PRMT10" "PFKFB3" "RBKS"
## [21] "CHD2" "ANKRD37" "MTND1P23" "PSMD6-AS2"
## [25] "KCNQ1OT1" "RP11-434H6.7"
## [1] 5
## [1] "ZNF419" "FAM45A" "RNF121" "NDUFAF6"
## [5] "TMSB15B" "CCDC28B" "ZBTB39" "RHEBL1"
## [9] "LRRC45" "RP11-23P13.6" "ZNF93" "ENTPD5"
## [13] "ZNF511" "ZNF525" "RP11-122G18.7" "AC115617.2"
## [17] "RP11-262H14.3" "AC007041.2" "AC004069.2" "MIR146A"
## [21] "RPPH1" "PMF1-BGLAP" "RP11-209D14.4" "AL358333.1"
## [25] "CTD-3214H19.4" "CTD-2545M3.2" "RP11-282O18.6"
## [1] 6
## [1] "NT5C2" "PMM1" "GALK1" "GNPTAB"
## [5] "STYXL1" "PGPEP1" "XAF1" "AHI1"
## [9] "CLSTN3" "WARS" "TATDN1" "TMPRSS3"
## [13] "DNAJC18" "TMEM107" "SPATA13" "PSMG1"
## [17] "TNFRSF18" "EFCAB7" "TRGV3" "RP11-64B16.2"
## [21] "RP11-247I13.3" "RP5-1053E7.3" "UBXN2B" "RP11-782C8.1"
## [25] "PSMC1P9" "EFTUD1P1"
## [1] 7
## [1] "MCM9" "TMEM241" "KHDC1" "IRF8"
## [5] "MPPE1" "SLAMF8" "FCRL3" "MGAT4B"
## [9] "AMDHD2" "LZTFL1" "PRIMPOL" "GNGT2"
## [13] "TRIM68" "NINJ2" "ZBTB8OS" "ABHD16B"
## [17] "PTGES3P2" "PHBP3" "GS1-124K5.2" "PA2G4P4"
## [21] "NPM1P34" "BDH2P1" "RP11-552M11.4" "MS4A1"
## [25] "SERHL2"
## [1] 8
## [1] "TRPT1" "TRBV4-2" "TRAV12-2" "RP11-383G10.3"
## [5] "RPS19P1" "NPM1P19" "Z97634.3" "RP11-32B5.1"
## [9] "NDUFA9P1" "RP11-33B1.1" "HNRNPA1P50" "DGKA"
## [13] "TCF7" "CCR7" "PCNXL2" "CDC42EP3"
## [17] "ZBTB20" "DENND5A" "POU6F1" "SELL"
## [21] "RPS26P6" "RP11-91K8.4" "WHAMMP2" "TMEM9B-AS1"
## [25] "RP11-747H7.3" "CTD-2017D11.1" "RP11-51J9.5"
## [1] 9
## [1] "APH1B" "SEC24D" "ATF4P3" "RPL7AP31"
## [5] "HNRNPA1P55" "HNRNPA1P16" "APBA2" "TMEM66"
## [9] "ZMAT1" "NPIPB3" "AC018720.10" "EIF1"
## [13] "NR1D2" "NPIPB4" "HLA-J" "RP11-572P18.1"
## [17] "MTND2P28" "CTD-2328D6.1" "RPL41" "ACTBP12"
## [21] "RPS3AP6" "HLA-W" "NPIPB5" "MTATP6P1"
## [25] "RP11-320M16.1" "CTD-2031P19.4"
## [1] 10
## [1] "SMG6" "DUSP12" "MICALL1" "CNOT2" "RCOR3" "MTFR1L"
## [7] "CCDC77" "METTL8" "FOPNL" "CASP1" "KSR1" "VPS37A"
## [13] "TMEM208" "TMEM126A" "CEP63" "CNOT10" "CEP57L1" "RN7SL749P"
## [19] "TNRC6C" "CLDND1" "TNRC6B" "CNOT6L" "BTG2" "RALGAPA1"
## [25] "PLA2G4B"
## [1] 11
## [1] "POLA2" "USP28" "WDR3" "WIPI1" "PIK3C3"
## [6] "ULK2" "WDR13" "IFIT3" "IFIT2" "L3HYPDH"
## [11] "RSAD2" "BCAS3" "PELP1" "BAP1" "WDR41"
## [16] "PHAX" "ATG13" "IFIT1" "PIK3R4" "MBD5"
## [21] "CATSPER2P1" "RAB12" "C9orf72" "FBXO32"
## [1] 12
## [1] "CD200" "OCEL1" "MS4A6A" "PDE6B"
## [5] "NUDT7" "TMEM138" "TMEM155" "C9orf89"
## [9] "GSTM4" "NME6" "EEF1GP1" "TMEM194B"
## [13] "RSC1A1" "AC009403.2" "RP3-340B19.5" "PGAM4"
## [17] "RP11-247I13.6" "AC090804.1" "BHLHE40-AS1" "GAPDHP2"
## [21] "FAM21FP" "KB-1507C5.2" "SF3A3P2" "AP000620.1"
## [25] "MTRNR2L3" "RP11-493L12.6" "AC006129.4"
## [1] 13
## [1] "TM7SF3" "MAP3K13" "POLD3" "AAAS"
## [5] "TIMM9" "PLA2G15" "POP4" "FAHD2A"
## [9] "GALE" "NR2C1" "TIMM10" "FHOD1"
## [13] "UCK2" "GALK2" "XRCC6BP1" "MEI1"
## [17] "POP5" "CTDNEP1" "DALRD3" "PIGW"
## [21] "WDR53" "UCKL1" "ABHD14A" "RP11-304L19.5"
## [25] "GGT7" "OBSCN"
## [1] 14
## [1] "CRTAM" "TFDP2" "IRF4" "KIR3DL1"
## [5] "TMEM134" "AC004840.9" "SMIM19" "FCRL6"
## [9] "SLC9A9" "FAM49A" "ZNF649" "NPM1P32"
## [13] "CD27-AS1" "RNU2-63P" "RP11-567G24.1" "PATL2"
## [17] "SEPT7P7" "GYG1P3" "BTF3P10" "ERP29P1"
## [21] "RP11-254B13.4" "AC011747.4" "STARD4-AS1" "GAPDHP38"
## [25] "RNU1-125P" "AL161784.1" "AOAH"
## [1] 15
## [1] "EVC" "LTBP4" "ARHGEF18" "SCRN2"
## [5] "GPN2" "OXSM" "FAM122B" "DBF4B"
## [9] "TAF10" "CCDC101" "ZBED2" "RP11-773D16.1"
## [13] "RP11-119F19.2" "AC093391.2" "MAK" "MAN1C1"
## [17] "ATXN7" "POLR2J3" "YPEL2" "TTC3"
## [21] "PLGLB1" "NELL2" "MIR4461" "GPRASP1"
## [25] "RP11-514P8.6" "LINC00944"
## [1] 16
## [1] "STAU2" "NOP16" "YBX3" "NTHL1" "SART3" "KHSRP"
## [7] "FMR1" "DOT1L" "DHX58" "DKC1" "APTX" "UTP23"
## [13] "HIST1H2BD" "MARS" "KBTBD2" "PCGF5" "ZFP62" "ZNF770"
## [19] "C9orf114" "ZBTB48" "MIR29B1" "PDCD4" "ZNF589" "TSPYL2"
## [1] 17
## [1] "C1orf112" "VPS41" "AGA" "BCL3" "RNF13" "CDKL1"
## [7] "GSR" "TYK2" "SNX8" "NCOA7" "FIGNL1" "TTLL4"
## [13] "IDH1" "TMOD3" "TAMM41" "WDR43" "COG5" "ETFDH"
## [19] "ZNF431" "ANKRD28" "TREX1" "IFRD2" "PPIL3" "PLXND1"
## [25] "SELM"
## [1] 18
## [1] "MAD1L1" "RNF10" "PTPN18" "GABPB1" "SMC4" "C3orf14"
## [7] "STK25" "CKS2" "CCNB1" "PMAIP1" "HIRIP3" "CCNB2"
## [13] "ANAPC10" "CTSB" "TBCA" "RRM2" "ASB8" "EDARADD"
## [19] "TDRD7" "HIST1H4C" "DDX3Y" "FAM117B" "NPAT" "PLK3"
## [25] "TSC22D2"
## [1] 19
## [1] "DYRK4" "ZNF684" "C2orf43" "DTD2"
## [5] "SLC35A5" "ZNF80" "ZNF678" "ZNF749"
## [9] "C10orf128" "TRAV16" "AC018804.7" "XXbac-B562F10.11"
## [13] "KIR2DS4" "AC012318.3" "GK3P" "GOT2P3"
## [17] "LINC00484" "AC002331.1" "RP11-305L7.3" "CTD-2301A4.3"
## [21] "AC005329.7" "RP11-473N11.2" "AP000462.1" "RP11-317N8.4"
## [25] "CD248" "CHRM3-AS2" "RP1-187B23.1" "RP11-1000B6.3"
## [1] 20
## [1] "RP3-324O17.4" "NSMCE4A" "NAP1L4P1" "MTHFD2P7"
## [5] "CCDC30" "TRBV20-1" "RP11-365H23.1" "AC009506.2"
## [9] "CNOT7P1" "ETF1P2" "RPL37P23" "HSPA8P4"
## [13] "CTC-436P18.1" "TRAV1-2" "RP11-511H9.4" "ANP32AP1"
## [17] "HMGB1P8" "RCAN3" "NEK1" "ACRC"
## [21] "FILIP1L" "TCEAL3" "AC084018.1" "LINC00674"
## [25] "RP11-44N11.1" "RP11-727F15.9" "QRSL1P3"
## [1] 21
## [1] "TBPL1" "DUS4L" "LOXL3" "FANCL"
## [5] "CD160" "DHDDS" "NPC2" "MCEE"
## [9] "MT2A" "MTHFS" "GTF2A2" "USF1"
## [13] "KIAA1841" "NFU1" "MT1E" "MT1X"
## [17] "TECPR1" "TRAV13-1" "TSTD1" "RNU2-2P"
## [21] "UBE2D3P2" "PET100" "LINC00493" "RP11-1012A1.7"
## [25] "MIR142"
## [1] 22
## [1] "GBA2" "DERL2" "ERGIC2" "RABGGTA" "ILVBL" "GOSR2"
## [7] "CPD" "SRM" "NQO2" "PPFIA1" "FADS2" "MAP3K6"
## [13] "LIMD1" "FADS1" "AMFR" "FRS2" "JSRP1" "PAAF1"
## [19] "NT5DC1" "CSNK1A1L" "AGER" "DKK3" "EPHA4" "MPP7"
## [25] "KLHL25"
## [1] 23
## [1] "ZNF268" "FAH" "ZNF85" "PECR"
## [5] "CCRL2" "MTERF" "RRNAD1" "ADCK5"
## [9] "SNHG11" "GEN1" "C2orf76" "ZNF257"
## [13] "ANAPC10P1" "RP4-694B14.5" "PIN4P1" "RP3-342P20.2"
## [17] "ZNF826P" "RPL13P5" "RN7SL56P" "TPM3P6"
## [21] "RNF138P1" "RP11-889L3.4" "RP11-844P9.3" "RP11-638I2.10"
## [25] "CTD-2022H16.3" "CTB-31O20.3" "RP11-297D21.4"
## [1] 24
## [1] "DEPDC5" "PIM2" "FGFBP2" "PPCDC"
## [5] "DEF8" "PPOX" "SPON2" "FCGR3B"
## [9] "CX3CR1" "ITGAM" "EIF2S3L" "FCGR3A"
## [13] "HIST2H2BF" "TRAV35" "RP11-270C12.3" "RPS12P26"
## [17] "SNRPEP4" "PTGES3P1" "FAM200B" "RP11-81H14.2"
## [21] "MIR3615" "LUZP6" "AC024592.12" "FRMD4A"
## [25] "PER1"
## [1] 25
## [1] "MFAP3" "TNFRSF9" "C14orf93" "SLC25A14" "SLC11A2"
## [6] "MDGA1" "CD86" "TNFSF10" "IFI6" "DPH6"
## [11] "IFI44L" "IFI44" "LAIR2" "TRANK1" "CXCR6"
## [16] "TRBV9" "TRAV19" "CRYGS" "AC104820.2" "MIR155HG"
## [21] "AC092580.4" "AKAP2" "CCL3L3" "RP11-345J4.6" "AMICA1"
## [26] "MUC20"
## [1] 26
## [1] "DHPS" "DHRS12" "ENO3" "PRR4" "PTP4A1"
## [6] "MYB" "CLU" "NARF" "MTF2" "SUV39H2"
## [11] "SFR1" "NAA15" "FBXO22" "SWI5" "RMDN1"
## [16] "BOLA1" "KATNA1" "DUSP28" "ZNF544" "WDHD1"
## [21] "RP13-638C3.4" "PMEPA1" "LEF1" "NAA16" "GOLGA8A"
## [1] 27
## [1] "REXO1" "ZNF683" "PDCL3P5" "AC098614.2"
## [5] "NPM1P33" "CALM2P3" "TCP1P1" "AC144530.1"
## [9] "CDC42P1" "RP3-395M20.8" "RP11-382J24.2" "HSPA8P5"
## [13] "AC006483.1" "AC139149.1" "MIR3661" "RASGRP2"
## [17] "CPQ" "FOXP1" "C1orf162" "PLAC8"
## [21] "FAM102A" "GPR183" "SATB1" "CTD-3092A11.1"
## [25] "RP11-632K20.7" "RP1-313I6.12"
## [1] 28
## [1] "CHI3L2" "PUS7L" "IL10" "XCL1"
## [5] "XCL2" "CMAHP" "ZNF720" "RPSAP54"
## [9] "LDHBP2" "MYL5" "RP11-2F9.3" "ARPC3P1"
## [13] "HNRNPKP2" "RPL19P21" "SKP1P1" "RPS11P5"
## [17] "EEF1A1P14" "RAB1C" "AP000476.1" "RPS19P3"
## [21] "AC018462.3" "EEF1A1P10" "RP11-179A18.1" "SRP14-AS1"
## [25] "RP11-686D22.10" "RP4-739H11.4" "AP001468.1"
## [1] 29
## [1] "GZMB" "GMPR2" "NHP2P1" "IL18RAP"
## [5] "PTGER2" "NARG2" "FUOM" "TNFAIP8L2"
## [9] "HOPX" "ARHGAP11B" "TRAV14DV4" "TRAV29DV5"
## [13] "RP13-383K5.4" "KANSL1-AS1" "RP4-742C19.12" "RP11-350G13.1"
## [17] "RP4-800M22.1" "PRDX3P1" "TPI1P2" "ADH5P4"
## [21] "RP11-446E9.1" "GAPDHP60" "RP11-402J6.3" "USP30-AS1"
## [25] "SNORD3A" "TPMTP1" "CTB-52I2.4"
## [1] 30
## [1] "EVI5" "CDKN3" "RAD51C" "STMN1"
## [5] "TXNDC17" "TROAP" "BORA" "GEMIN6"
## [9] "MITD1" "PAQR4" "CDCA7L" "C11orf82"
## [13] "ZFYVE19" "UBE2C" "TYMS" "LRTOMT"
## [17] "SESTD1" "TCTEX1D2" "NCKIPSD" "MDP1"
## [21] "RP11-378G13.2" "SAPCD1" "PAICSP4" "HMGB1P24"
## [25] "RP11-307P22.1" "RP11-265N6.2"
## [1] 31
## [1] "P2RX5" "PRMT7" "SNX14" "PWP1" "ACTL6A" "PRSS23"
## [7] "CXXC1" "TOMM40L" "B2M" "CAPN12" "AFMID" "KNTC1"
## [13] "TMEM120A" "TMSB4X" "RGPD5" "PPP2R5C" "STK17B" "PPIL4"
## [19] "BTG1" "SSH2" "EPHA1" "PIP4K2A" "CXCR5" "PPP1R10"
## [25] "MALAT1"
## [1] 32
## [1] "GLT8D1" "FAR2" "SH3BP2" "KIF4A" "MAN2B1" "IFNG"
## [7] "SCPEP1" "DNPEP" "COQ3" "TPGS2" "SPPL2A" "LPP"
## [13] "TIFA" "MX1" "CCDC51" "SLC39A13" "PRF1" "CADM1"
## [19] "GM2A" "HIST1H4J" "HLA-DRA" "NCR3" "DNASE1" "ATP5J2"
## [25] "LMO7"
## [1] 33
## [1] "ERCC2" "GTF2H3" "NPL" "DRAM2" "NTAN1"
## [6] "C19orf55" "ZNF613" "ZNF765" "RUFY2" "POTEKP"
## [11] "TRGV10" "TRGV5" "TRAV8-2" "TRAV24" "TRGC2"
## [16] "TSEN15P1" "TRGV2" "CTC-338M12.4" "RP11-693N9.2" "ZEB1-AS1"
## [21] "LINC00426" "RP4-728D4.2" "PVT1" "TRGV7" "SCML1"
## [26] "RP13-488H8.1" "SLC7A5P1"
## [1] 34
## [1] "IMP4" "RPS17" "RPL34" "RPS12" "RPS25" "RPL21" "RPL5" "RPS10"
## [9] "RPS2" "RPL13A" "RPS27A" "RPL32" "RPS3A" "RPL7" "RPS3" "RPL30"
## [17] "RPL9" "RPS14" "RPL27A" "RPLP2" "RPS27" "RPS23" "RPS26" "RPL23A"
## [25] "RPS18"
## [1] 35
## [1] "OAS1" "MFSD9" "IFI27" "EFCAB4A"
## [5] "LCORL" "ZNF28" "CPT1B" "METTL6"
## [9] "TRDV1" "TRDC" "NAP1L1P3" "RP11-12M9.4"
## [13] "PSMA6P1" "LYPLA1P3" "CCT8P1" "HNRNPA1P21"
## [17] "RP11-288E14.2" "RBBP4P1" "GMPSP1" "RP11-613F22.5"
## [21] "RBBP4P5" "RP11-416A17.6" "TRAV30" "RP11-265N6.3"
## [25] "ATP5A1P3" "ACTBP9" "RP11-1094M14.7"
## [1] 36
## [1] "UBXN8" "SLC12A4" "YIPF2" "SLC41A2" "LINS" "MFSD6" "TMEM237"
## [8] "ALG8" "C2orf44" "GLB1" "LGALS9C" "SLC38A9" "YIPF6" "DBNDD2"
## [15] "PIK3IP1" "SLC38A1" "UAP1" "YPEL5" "NBPF14" "SLC38A2" "EPB41"
## [22] "NBPF10" "RGPD6" "CD55" "FAM169A" "NBPF16"
## [1] 37
## [1] "ICA1" "MED24" "NSMAF" "ZNRD1" "REC8" "POLR2I"
## [7] "LIG1" "POLE4" "EPAS1" "AKR1A1" "UXT" "CHTF18"
## [13] "SLC2A8" "TBCD" "PPP4R1" "MED11" "POLR2H" "IL15"
## [19] "MZT2A" "POLE" "PPARA" "CHAMP1" "STK19" "C17orf89"
## [25] "MRPL33"
## [1] 38
## [1] "RABGAP1" "CD84" "RGS1" "HAVCR1"
## [5] "EGR2" "TEP1" "TMEM19" "FAM50B"
## [9] "NAALADL1" "THAP2" "SH2D1B" "SGMS1"
## [13] "TRAV21" "MAPKAPK5-AS1" "RP11-271C24.3" "WDR65"
## [17] "CTB-4E7.1" "CTD-2521M24.9" "RP11-705C15.5" "ABLIM1"
## [21] "RIMKLB" "PHLDB3" "LDOC1" "KLRK1"
## [25] "HCG4P5" "ATP1B3-AS1"
## [1] 39
## [1] "NDUFAF7" "ACADVL" "NFE2L1" "MTIF2" "MRPS33" "NDUFAF5"
## [7] "CDK5RAP1" "EARS2" "MTFMT" "THG1L" "ATPAF1" "C6orf203"
## [13] "MTO1" "MRRF" "CETN3" "MALSU1" "MRPL55" "NDUFS4"
## [19] "C7orf55" "MRPL48" "ZNF782" "OXLD1" "CCDC109B" "TSHZ2"
## [1] 40
## [1] "MBNL3" "DDX49" "PDZD2" "RPSAP47"
## [5] "RP1-102E24.1" "UBA52P6" "RP1-182O16.1" "RPL19P12"
## [9] "RP11-350G8.3" "RPSAP4" "MGAT4A" "HECA"
## [13] "C1orf63" "PLXDC1" "TRABD2A" "RPS3AP26"
## [17] "AC021593.1" "LTB" "RPL10P3" "RPL9P8"
## [21] "RPL3P4" "RPL9P9" "RPL9P7" "RP11-285F7.2"
## [25] "MTND4P12" "ZNF10" "RP11-335G20.7"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_2"
## [1] "IL4R" "UTP6" "ACVR1" "SMUG1" "GLUL"
## [6] "GNG4" "ZNF816" "RPS27AP2" "CTB-33G10.1" "TXK"
## [11] "ARRDC2" "RASGRF2" "EGR1" "ACVR2A" "FOSB"
## [16] "JUND" "SKIL" "SORL1" "SGSM2" "GNAQ"
## [21] "LDLRAP1" "DHRS3" "TC2N" "TMEM150A" "DNHD1"
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 3547 response to bmp 5.727704e-06 0.9999999
## numDEInCat numInCat FDR
## 3547 5 11 0.02340913
##
## [1] "set_4"
## [1] "ID3" "PARP2" "MMS22L" "PLIN2"
## [5] "ATF3" "HIST1H2BC" "PLA2G6" "HIST2H2AA4"
## [9] "HIST1H2BN" "HIST1H3G" "RP11-386G11.10" "IFRD1"
## [13] "RGCC" "NR4A3" "RASGEF1B" "NR4A2"
## [17] "TIPARP" "PRMT10" "PFKFB3" "RBKS"
## [21] "CHD2" "ANKRD37" "MTND1P23" "PSMD6-AS2"
## [25] "KCNQ1OT1" "RP11-434H6.7"
## $reactome
## category
## 786 runx1 regulates genes involved in megakaryocyte differentiation and platelet function
## 10 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 63 assembly of the orc complex at the origin of replication
## 122 chromatin modifications during the maternal to zygotic transition mzt
## 209 dna methylation
## 249 ercc6 csb and ehmt2 g9a positively regulate rrna expression
## 746 rho gtpases activate pkns
## 879 sirt1 negatively regulates rrna expression
## 639 prc2 methylates histones and dna
## 285 formation of the beta catenin tcf transactivating complex
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 786 4.313170e-06 0.9999999 5 13
## 10 2.519897e-05 0.9999996 4 9
## 63 2.519897e-05 0.9999996 4 9
## 122 2.519897e-05 0.9999996 4 9
## 209 2.519897e-05 0.9999996 4 9
## 249 2.519897e-05 0.9999996 4 9
## 746 2.519897e-05 0.9999996 4 9
## 879 2.519897e-05 0.9999996 4 9
## 639 4.141248e-05 0.9999991 4 10
## 285 6.416829e-05 0.9999984 4 11
## FDR
## 786 0.003219168
## 10 0.003219168
## 63 0.003219168
## 122 0.003219168
## 209 0.003219168
## 249 0.003219168
## 746 0.003219168
## 879 0.003219168
## 639 0.004702617
## 285 0.005961818
##
## $immune
## category over_represented_pvalue
## 1235 gse17974 0h vs 0.5h in vitro act cd4 tcell dn 2.969641e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 1235 1 6 15 0.00151422
##
## [1] "set_8"
## [1] "TRPT1" "TRBV4-2" "TRAV12-2" "RP11-383G10.3"
## [5] "RPS19P1" "NPM1P19" "Z97634.3" "RP11-32B5.1"
## [9] "NDUFA9P1" "RP11-33B1.1" "HNRNPA1P50" "DGKA"
## [13] "TCF7" "CCR7" "PCNXL2" "CDC42EP3"
## [17] "ZBTB20" "DENND5A" "POU6F1" "SELL"
## [21] "RPS26P6" "RP11-91K8.4" "WHAMMP2" "TMEM9B-AS1"
## [25] "RP11-747H7.3" "CTD-2017D11.1" "RP11-51J9.5"
## $immune
## category
## 56 goldrath eff vs memory cd8 tcell dn
## 3792 gse40274 ctrl vs eos transduced activated cd4 tcell dn
## 4851 gse9650 naive vs eff cd8 tcell up
## 4974 kaech naive vs day8 eff cd8 tcell up
## 2082 gse23568 ctrl vs id3 transduced cd8 tcell up
## 4086 gse43863 day6 eff vs day150 mem ly6c int cxcr5pos cd4 tcell dn
## 4844 gse9650 effector vs memory cd8 tcell dn
## 4969 kaech day8 eff vs memory cd8 tcell dn
## 2079 gse23568 ctrl transduced vs wt cd8 tcell dn
## 2746 gse2935 uv inactivated vs live sendai virus inf macrophage up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 56 5.535430e-06 0.9999999 5 23
## 3792 8.549934e-06 0.9999998 5 25
## 4851 1.261357e-05 0.9999996 5 27
## 4974 1.275095e-05 0.9999996 5 27
## 2082 2.443384e-05 0.9999995 4 15
## 4086 3.363985e-05 0.9999992 4 16
## 4844 4.275140e-05 0.9999982 5 34
## 4969 4.302329e-05 0.9999982 5 34
## 2079 5.471493e-05 0.9999985 4 18
## 2746 5.565429e-05 0.9999985 4 18
## FDR
## 56 0.01625427
## 3792 0.01625427
## 4851 0.01625427
## 4974 0.01625427
## 2082 0.02491763
## 4086 0.02742197
## 4844 0.02742197
## 4969 0.02742197
## 2079 0.02837812
## 2746 0.02837812
##
## [1] "set_10"
## [1] "SMG6" "DUSP12" "MICALL1" "CNOT2" "RCOR3" "MTFR1L"
## [7] "CCDC77" "METTL8" "FOPNL" "CASP1" "KSR1" "VPS37A"
## [13] "TMEM208" "TMEM126A" "CEP63" "CNOT10" "CEP57L1" "RN7SL749P"
## [19] "TNRC6C" "CLDND1" "TNRC6B" "CNOT6L" "BTG2" "RALGAPA1"
## [25] "PLA2G4B"
## $reactome
## category
## 981 transcriptional regulation by tp53
## 952 tp53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
## 954 tp53 regulates transcription of cell cycle genes
## 172 deadenylation of mrna
## 171 deadenylation dependent mrna decay
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 981 2.090452e-06 0.9999999 7 35
## 952 2.226282e-06 1.0000000 4 6
## 954 1.011921e-05 0.9999999 4 8
## 172 3.489845e-05 0.9999998 3 4
## 171 1.709831e-04 0.9999977 3 6
## FDR
## 981 0.001137630
## 952 0.001137630
## 954 0.003447277
## 172 0.008916553
## 171 0.034948947
##
## $go_bp
## category
## 1917 nuclear transcribed mrna poly a tail shortening
## 1912 nuclear transcribed mrna catabolic process
## 1913 nuclear transcribed mrna catabolic process deadenylation dependent decay
## 3702 rna destabilization
## 1372 mrna catabolic process
## 2380 positive regulation of mrna metabolic process
## 3201 regulation of mrna catabolic process
## 3700 rna catabolic process
## 3202 regulation of mrna metabolic process
## 1456 negative regulation of amide metabolic process
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1917 2.977880e-09 1.0000000 6 8
## 1912 1.120755e-08 1.0000000 7 15
## 1913 2.182607e-08 1.0000000 6 10
## 3702 2.834440e-07 1.0000000 6 14
## 1372 5.185335e-07 1.0000000 7 24
## 2380 7.335956e-07 1.0000000 6 16
## 3201 1.124232e-06 1.0000000 6 17
## 3700 2.188583e-06 0.9999999 7 29
## 3202 4.655463e-06 0.9999998 6 21
## 1456 3.558517e-05 0.9999979 6 29
## FDR
## 1917 1.217060e-05
## 1912 2.290263e-05
## 1913 2.973439e-05
## 3702 2.896089e-04
## 1372 4.238493e-04
## 2380 4.997009e-04
## 3201 6.563908e-04
## 3700 1.118092e-03
## 3202 2.114097e-03
## 1456 1.454366e-02
##
## [1] "set_11"
## [1] "POLA2" "USP28" "WDR3" "WIPI1" "PIK3C3"
## [6] "ULK2" "WDR13" "IFIT3" "IFIT2" "L3HYPDH"
## [11] "RSAD2" "BCAS3" "PELP1" "BAP1" "WDR41"
## [16] "PHAX" "ATG13" "IFIT1" "PIK3R4" "MBD5"
## [21] "CATSPER2P1" "RAB12" "C9orf72" "FBXO32"
## $go_bp
## category over_represented_pvalue
## 2830 regulation of autophagy 1.512986e-06
## 154 autophagosome organization 2.206566e-06
## 4025 vacuole organization 6.714553e-06
## 1173 macroautophagy 8.685364e-06
## 2684 protein localization to phagophore assembly site 1.772104e-05
## 3639 response to starvation 6.471983e-05
## 1924 nucleophagy 6.891717e-05
## 3142 regulation of macroautophagy 8.208376e-05
## 1171 lysosomal transport 8.238985e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2830 0.9999999 7 25 0.004509117
## 154 1.0000000 5 10 0.004509117
## 4025 0.9999998 5 12 0.008874270
## 1173 0.9999996 6 21 0.008874270
## 2684 1.0000000 3 3 0.014485176
## 3639 0.9999969 5 18 0.037414148
## 1924 0.9999996 3 4 0.037414148
## 3142 0.9999977 4 10 0.037414148
## 1171 0.9999977 4 10 0.037414148
##
## [1] "set_18"
## [1] "MAD1L1" "RNF10" "PTPN18" "GABPB1" "SMC4" "C3orf14"
## [7] "STK25" "CKS2" "CCNB1" "PMAIP1" "HIRIP3" "CCNB2"
## [13] "ANAPC10" "CTSB" "TBCA" "RRM2" "ASB8" "EDARADD"
## [19] "TDRD7" "HIST1H4C" "DDX3Y" "FAM117B" "NPAT" "PLK3"
## [25] "TSC22D2"
## $reactome
## category over_represented_pvalue
## 138 condensation of prometaphase chromosomes 1.472594e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 138 1 3 3 0.01504991
##
## [1] "set_21"
## [1] "TBPL1" "DUS4L" "LOXL3" "FANCL"
## [5] "CD160" "DHDDS" "NPC2" "MCEE"
## [9] "MT2A" "MTHFS" "GTF2A2" "USF1"
## [13] "KIAA1841" "NFU1" "MT1E" "MT1X"
## [17] "TECPR1" "TRAV13-1" "TSTD1" "RNU2-2P"
## [21] "UBE2D3P2" "PET100" "LINC00493" "RP11-1012A1.7"
## [25] "MIR142"
## $reactome
## category over_represented_pvalue
## 485 metallothioneins bind metals 9.853714e-06
## 737 response to metal ions 9.853714e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 485 1 3 3 0.005035248
## 737 1 3 3 0.005035248
##
## $go_bp
## category over_represented_pvalue
## 353 cellular response to cadmium ion 1.502551e-05
## 358 cellular response to copper ion 1.502551e-05
## 564 detoxification of copper ion 1.502551e-05
## 565 detoxification of inorganic compound 1.502551e-05
## 3548 response to cadmium ion 1.502551e-05
## 3555 response to copper ion 1.502551e-05
## 1055 intracellular zinc ion homeostasis 5.835770e-05
## 420 cellular response to zinc ion 5.864869e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 353 1.0000000 3 3 0.01023488
## 358 1.0000000 3 3 0.01023488
## 564 1.0000000 3 3 0.01023488
## 565 1.0000000 3 3 0.01023488
## 3548 1.0000000 3 3 0.01023488
## 3555 1.0000000 3 3 0.01023488
## 1055 0.9999997 3 4 0.02996215
## 420 0.9999997 3 4 0.02996215
##
## [1] "set_25"
## [1] "MFAP3" "TNFRSF9" "C14orf93" "SLC25A14" "SLC11A2"
## [6] "MDGA1" "CD86" "TNFSF10" "IFI6" "DPH6"
## [11] "IFI44L" "IFI44" "LAIR2" "TRANK1" "CXCR6"
## [16] "TRBV9" "TRAV19" "CRYGS" "AC104820.2" "MIR155HG"
## [21] "AC092580.4" "AKAP2" "CCL3L3" "RP11-345J4.6" "AMICA1"
## [26] "MUC20"
## $immune
## category over_represented_pvalue
## 4555 gse6269 healthy vs staph aureus inf pbmc up 4.004366e-06
## 2427 gse2706 2h vs 8h r848 stim dc dn 1.417185e-05
## 1337 gse18791 ctrl vs newcastle virus dc 6h dn 2.301492e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4555 0.9999998 6 22 0.02041826
## 2427 0.9999995 5 16 0.03613114
## 1337 0.9999987 6 29 0.03911769
##
## [1] "set_27"
## [1] "REXO1" "ZNF683" "PDCL3P5" "AC098614.2"
## [5] "NPM1P33" "CALM2P3" "TCP1P1" "AC144530.1"
## [9] "CDC42P1" "RP3-395M20.8" "RP11-382J24.2" "HSPA8P5"
## [13] "AC006483.1" "AC139149.1" "MIR3661" "RASGRP2"
## [17] "CPQ" "FOXP1" "C1orf162" "PLAC8"
## [21] "FAM102A" "GPR183" "SATB1" "CTD-3092A11.1"
## [25] "RP11-632K20.7" "RP1-313I6.12"
## $immune
## category
## 595 gse14699 naive vs deletional tolerance cd8 tcell dn
## 1580 gse20727 h2o2 vs ros inhibitor treated dc up
## 3848 gse40274 lef1 vs foxp3 and lef1 transduced activated cd4 tcell dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 595 2.973401e-08 1.0000000 6 25
## 1580 1.997739e-05 0.9999996 4 19
## 3848 2.494993e-05 0.9999995 4 20
## FDR
## 595 0.0001516137
## 1580 0.0424065620
## 3848 0.0424065620
##
## [1] "set_30"
## [1] "EVI5" "CDKN3" "RAD51C" "STMN1"
## [5] "TXNDC17" "TROAP" "BORA" "GEMIN6"
## [9] "MITD1" "PAQR4" "CDCA7L" "C11orf82"
## [13] "ZFYVE19" "UBE2C" "TYMS" "LRTOMT"
## [17] "SESTD1" "TCTEX1D2" "NCKIPSD" "MDP1"
## [21] "RP11-378G13.2" "SAPCD1" "PAICSP4" "HMGB1P24"
## [25] "RP11-307P22.1" "RP11-265N6.2"
## $immune
## category
## 4962 howard nk cell inact monov influenza a indonesia 05 2005 h5n1 age 18 49yo 3dy up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4962 7.935581e-07 1 5 10
## FDR
## 4962 0.004046353
##
## [1] "set_32"
## [1] "GLT8D1" "FAR2" "SH3BP2" "KIF4A" "MAN2B1" "IFNG"
## [7] "SCPEP1" "DNPEP" "COQ3" "TPGS2" "SPPL2A" "LPP"
## [13] "TIFA" "MX1" "CCDC51" "SLC39A13" "PRF1" "CADM1"
## [19] "GM2A" "HIST1H4J" "HLA-DRA" "NCR3" "DNASE1" "ATP5J2"
## [25] "LMO7"
## $go_bp
## category over_represented_pvalue
## 2895 regulation of cell killing 4.566378e-06
## 2172 positive regulation of cell killing 7.711744e-06
## 314 cell killing 2.617120e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2895 0.9999998 6 22 0.01575895
## 2172 0.9999998 5 14 0.01575895
## 314 0.9999985 6 29 0.03565390
##
## $immune
## category over_represented_pvalue
## 3539 gse37605 treg vs tconv c57bl6 foxp3 fusion gfp dn 1.925098e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 3539 1 5 10 0.009816073
##
## [1] "set_33"
## [1] "ERCC2" "GTF2H3" "NPL" "DRAM2" "NTAN1"
## [6] "C19orf55" "ZNF613" "ZNF765" "RUFY2" "POTEKP"
## [11] "TRGV10" "TRGV5" "TRAV8-2" "TRAV24" "TRGC2"
## [16] "TSEN15P1" "TRGV2" "CTC-338M12.4" "RP11-693N9.2" "ZEB1-AS1"
## [21] "LINC00426" "RP4-728D4.2" "PVT1" "TRGV7" "SCML1"
## [26] "RP13-488H8.1" "SLC7A5P1"
## $reactome
## category over_represented_pvalue
## 283 formation of rna pol ii elongation complex 0.0001637134
## 286 formation of the early elongation complex 0.0001637134
## 370 hiv transcription elongation 0.0001637134
## 506 mrna capping 0.0001637134
## 766 rna polymerase i transcription initiation 0.0001681170
## 767 rna polymerase i transcription termination 0.0001681170
## 371 hiv transcription initiation 0.0003302842
## 768 rna polymerase ii pre transcription events 0.0003302842
## 970 transcription of the hiv genome 0.0003302842
## 281 formation of incision complex in gg ner 0.0003557590
## under_represented_pvalue numDEInCat numInCat FDR
## 283 0.9999997 2 5 0.02863592
## 286 0.9999997 2 5 0.02863592
## 370 0.9999997 2 5 0.02863592
## 506 0.9999997 2 5 0.02863592
## 766 0.9999997 2 5 0.02863592
## 767 0.9999997 2 5 0.02863592
## 371 0.9999991 2 7 0.03635857
## 768 0.9999991 2 7 0.03635857
## 970 0.9999991 2 7 0.03635857
## 281 0.9999990 2 7 0.03635857
##
## [1] "set_34"
## [1] "IMP4" "RPS17" "RPL34" "RPS12" "RPS25" "RPL21" "RPL5" "RPS10"
## [9] "RPS2" "RPL13A" "RPS27A" "RPL32" "RPS3A" "RPL7" "RPS3" "RPL30"
## [17] "RPL9" "RPS14" "RPL27A" "RPLP2" "RPS27" "RPS23" "RPS26" "RPL23A"
## [25] "RPS18"
## $reactome
## category
## 21 activation of the mrna upon binding of the cap binding complex and eifs and subsequent binding to 43s
## 117 cellular response to starvation
## 255 eukaryotic translation elongation
## 256 eukaryotic translation initiation
## 387 influenza infection
## 471 metabolism of amino acids and derivatives
## 547 nonsense mediated decay nmd
## 691 regulation of expression of slits and robos
## 734 response of eif2ak4 gcn2 to amino acid deficiency
## 783 rrna processing
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat FDR
## 21 0 1 13 15 0
## 117 0 1 24 33 0
## 255 0 1 24 31 0
## 256 0 1 24 30 0
## 387 0 1 24 37 0
## 471 0 1 24 42 0
## 547 0 1 24 31 0
## 691 0 1 24 31 0
## 734 0 1 24 30 0
## 783 0 1 25 40 0
##
## $go_bp
## category over_represented_pvalue
## 515 cytoplasmic translation 0.000000e+00
## 3693 ribosome biogenesis 1.928974e-09
## 3691 ribosomal small subunit biogenesis 7.669988e-09
## 3718 rrna metabolic process 1.025484e-05
## 3692 ribosome assembly 2.168596e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 515 1.0000000 24 33 0.000000e+00
## 3693 1.0000000 11 35 3.941858e-06
## 3691 1.0000000 8 16 1.044908e-05
## 3718 0.9999994 7 26 1.047789e-02
## 3692 0.9999997 4 6 1.772611e-02
##
## $immune
## category
## 54 gaucher pbmc yf vax stamaril unknown age 7dy dn
## 463 gse14000 translated rna vs mrna dc dn
## 1628 gse2124 ctrl vs lymphotoxin beta treated mln up
## 1944 gse22886 naive bcell vs neutrophil up
## 1974 gse22886 naive tcell vs dc up
## 2104 gse2405 0h vs 24h a phagocytophilum stim neutrophil up
## 2109 gse2405 0h vs 9h a phagocytophilum stim neutrophil dn
## 3108 gse34205 healthy vs flu inf infant pbmc up
## 4014 gse41978 id2 ko vs id2 ko and bim ko klrg1 low effector cd8 tcell dn
## 4016 gse41978 klrg1 high vs low effector cd8 tcell dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat FDR
## 54 0 1 14 32 0
## 463 0 1 12 26 0
## 1628 0 1 10 19 0
## 1944 0 1 11 25 0
## 1974 0 1 14 33 0
## 2104 0 1 19 40 0
## 2109 0 1 19 37 0
## 3108 0 1 12 25 0
## 4014 0 1 12 32 0
## 4016 0 1 14 30 0
##
## [1] "set_36"
## [1] "UBXN8" "SLC12A4" "YIPF2" "SLC41A2" "LINS" "MFSD6" "TMEM237"
## [8] "ALG8" "C2orf44" "GLB1" "LGALS9C" "SLC38A9" "YIPF6" "DBNDD2"
## [15] "PIK3IP1" "SLC38A1" "UAP1" "YPEL5" "NBPF14" "SLC38A2" "EPB41"
## [22] "NBPF10" "RGPD6" "CD55" "FAM169A" "NBPF16"
## $reactome
## category
## 880 slc mediated transmembrane transport
## 997 transport of inorganic cations anions and amino acids oligopeptides
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 880 1.686105e-05 0.9999997 4 9
## 997 7.902577e-05 0.9999993 3 5
## FDR
## 880 0.01723200
## 997 0.04038217
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 864 glutamine transport 1.0726e-05 1
## numDEInCat numInCat FDR
## 864 3 3 0.04383717
##
## [1] "set_39"
## [1] "NDUFAF7" "ACADVL" "NFE2L1" "MTIF2" "MRPS33" "NDUFAF5"
## [7] "CDK5RAP1" "EARS2" "MTFMT" "THG1L" "ATPAF1" "C6orf203"
## [13] "MTO1" "MRRF" "CETN3" "MALSU1" "MRPL55" "NDUFS4"
## [19] "C7orf55" "MRPL48" "ZNF782" "OXLD1" "CCDC109B" "TSHZ2"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 495 mitochondrial translation 5.271263e-09 1.0000000
## 986 translation 3.177704e-05 0.9999979
## numDEInCat numInCat FDR
## 495 6 9 5.387230e-06
## 986 7 46 1.623806e-02
##
## $go_bp
## category over_represented_pvalue
## 1301 mitochondrial gene expression 0.000000e+00
## 1311 mitochondrial translation 3.526225e-09
## 1307 mitochondrial rna metabolic process 9.799058e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 1301 1.0000000 9 16 0.000000e+00
## 1311 1.0000000 7 13 7.205842e-06
## 1307 0.9999999 4 7 1.334958e-02
##
## $immune
## category
## 4823 gse9316 cd4 tcell balbc vs th17 enri cd4 tcell skg pma iono stim fr4neg up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4823 9.056117e-06 0.9999997 5 14
## FDR
## 4823 0.04617714
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8958692 478.5 17165476 916.8 NA 17165476 916.8
## Vcells 19171056 146.3 57891911 441.7 65536 78485130 598.8
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] goseq_1.50.0
## [12] geneLenDataBase_1.34.0
## [13] BiasedUrn_2.0.10
## [14] fgsea_1.24.0
## [15] biomaRt_2.54.1
## [16] limma_3.54.2
## [17] tidyr_1.3.0
## [18] ggpubr_0.6.0
## [19] ggplot2_3.4.2
## [20] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 tools_4.2.3
## [9] backports_1.4.1 bslib_0.4.2
## [11] utf8_1.2.3 R6_2.5.1
## [13] mgcv_1.8-42 DBI_1.1.3
## [15] colorspace_2.1-0 withr_2.5.0
## [17] tidyselect_1.2.0 prettyunits_1.1.1
## [19] bit_4.0.5 curl_5.0.1
## [21] compiler_4.2.3 cli_3.6.1
## [23] xml2_1.3.4 DelayedArray_0.24.0
## [25] rtracklayer_1.58.0 sass_0.4.5
## [27] scales_1.2.1 rappdirs_0.3.3
## [29] Rsamtools_2.14.0 stringr_1.5.0
## [31] digest_0.6.31 rmarkdown_2.21
## [33] XVector_0.38.0 pkgconfig_2.0.3
## [35] htmltools_0.5.5 MatrixGenerics_1.10.0
## [37] dbplyr_2.3.2 fastmap_1.1.1
## [39] rlang_1.1.0 rstudioapi_0.14
## [41] RSQLite_2.3.1 BiocIO_1.8.0
## [43] jquerylib_0.1.4 generics_0.1.3
## [45] jsonlite_1.8.4 BiocParallel_1.32.6
## [47] dplyr_1.1.2 car_3.1-2
## [49] RCurl_1.98-1.12 magrittr_2.0.3
## [51] GO.db_3.16.0 GenomeInfoDbData_1.2.9
## [53] Matrix_1.6-4 Rcpp_1.0.10
## [55] munsell_0.5.0 fansi_1.0.4
## [57] abind_1.4-5 lifecycle_1.0.3
## [59] stringi_1.7.12 yaml_2.3.7
## [61] carData_3.0-5 SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0 BiocFileCache_2.6.1
## [65] grid_4.2.3 blob_1.2.4
## [67] parallel_4.2.3 crayon_1.5.2
## [69] lattice_0.20-45 splines_4.2.3
## [71] Biostrings_2.66.0 cowplot_1.1.1
## [73] hms_1.1.3 KEGGREST_1.38.0
## [75] knitr_1.44 pillar_1.9.0
## [77] rjson_0.2.21 ggsignif_0.6.4
## [79] codetools_0.2-19 fastmatch_1.1-3
## [81] XML_3.99-0.14 glue_1.6.2
## [83] evaluate_0.20 png_0.1-8
## [85] vctrs_0.6.2 gtable_0.3.3
## [87] purrr_1.0.1 cachem_1.0.7
## [89] xfun_0.39 broom_1.0.4
## [91] restfulr_0.0.15 rstatix_0.7.2
## [93] tibble_3.2.1 GenomicAlignments_1.34.1
## [95] memoise_2.0.1